railroadtracks
Introduction
Installation
Requirements
Installation
Tutorial
Creating a project
Displaying a project
Working with model environments
Aligning reads using bowtie2
Task execution
The graph in the dependency graph
Building a full pipeline
Building blocks for the pipeline
1/4: Align the reads
2/4: Quantify the alignments
3/4: Build a table of counts
4/4: Save unaligned reads into FASTQ files
Assembly of the pipeline
Handling results (target assets)
Results from one task
Handling several alternative results
Cookbook
Environment
Checking that 3rd-party executables are present
Project
Get all tasks of a given type
Get all tasks matching a list of types
Get all tasks fulfilling a given activity
TaskSet
Subset all tasks with a given status
Subset all tasks ready for execution
Get all child tasks for a
TaskSet
TaskSetGraph
Execute all tasks
Recipes
Steps and assets
Concept
Unspecified assets
Notes about the design
Setup
Simple recipe
Loops, nested loops, and many variants
Docstrings
Troubleshooting
Model
Overview
Activities
Inheritance diagram
Docstrings
Extending the framework
Writing custom steps
Simple case
Steps performing several activities
Unified execution
Unified execution
Version number
Running a step
Using a scheduler/Queueing system
Docstrings
Persistence
railroadtracks
Docs
»
Index
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A
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B
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C
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D
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E
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F
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G
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I
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M
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N
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P
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R
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S
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T
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U
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V
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W
_
__init__() (railroadtracks.easy.Environment method)
(railroadtracks.easy.Project method)
A
activities (railroadtracks.easy.Environment attribute)
ACTIVITY (class in railroadtracks.rnaseq)
ActivityCount (class in railroadtracks.easy)
add() (railroadtracks.hortator.StepGraph method)
add_task() (railroadtracks.easy.Project method)
Asset (class in railroadtracks.easy)
Assets (railroadtracks.rnaseq.CRCHeadTail attribute)
AssetsCRCHeadTail (class in railroadtracks.rnaseq)
B
build_AssetSet() (in module railroadtracks.unifex)
C
cache (railroadtracks.easy.Project attribute)
Call (class in railroadtracks.unifex)
call_factory() (in module railroadtracks.easy)
cleantargets_stepconcrete() (railroadtracks.hortator.StepGraph method)
clsname (railroadtracks.hortator.PersistentTaskGraph.StoredEntityNoLabel attribute)
count (railroadtracks.easy.ActivityCount attribute)
CRCHeadTail (class in railroadtracks.rnaseq)
D
db_fn (railroadtracks.easy.Project attribute)
DbID (class in railroadtracks.hortator)
destinationwalk_stepconcrete() (railroadtracks.hortator.StepGraph method)
destinationwalk_storedentity() (railroadtracks.hortator.StepGraph method)
E
entity (railroadtracks.easy.Asset attribute)
entityname (railroadtracks.hortator.PersistentTaskGraph.StoredEntityNoLabel attribute)
Environment (class in railroadtracks.easy)
execute() (railroadtracks.unifex.Call method)
F
finalsteps() (railroadtracks.hortator.PersistentTaskGraph method)
G
get_parenttask_of_storedentity() (railroadtracks.hortator.PersistentTaskGraph method)
get_sourcesofactivity() (railroadtracks.hortator.PersistentTaskGraph method)
get_srcassets() (railroadtracks.hortator.PersistentTaskGraph method)
get_targetassets() (railroadtracks.hortator.PersistentTaskGraph method)
get_targetsofactivity() (railroadtracks.easy.Project method)
(railroadtracks.hortator.PersistentTaskGraph method)
get_targetsoftype() (railroadtracks.easy.Project method)
(railroadtracks.hortator.PersistentTaskGraph method)
get_targetstepconcrete() (railroadtracks.hortator.PersistentTaskGraph method)
get_task() (railroadtracks.easy.Project method)
get_tasksoftype() (railroadtracks.easy.Project method)
get_taskswithactivity() (railroadtracks.easy.Project method)
I
id (railroadtracks.hortator.DbID attribute)
(railroadtracks.hortator.PersistentTaskGraph.StoredEntityNoLabel attribute)
id_step_activity() (railroadtracks.hortator.PersistentTaskGraph method)
id_step_type() (railroadtracks.hortator.PersistentTaskGraph method)
id_step_variant() (railroadtracks.hortator.PersistentTaskGraph method)
id_stepconcrete() (railroadtracks.hortator.PersistentTaskGraph method)
id_stepparameters() (railroadtracks.hortator.PersistentTaskGraph method)
id_stored_entity() (railroadtracks.hortator.PersistentTaskGraph method)
id_stored_sequence() (railroadtracks.hortator.PersistentTaskGraph method)
iter_finaltargets() (railroadtracks.hortator.PersistentTaskGraph method)
iter_srcassets() (railroadtracks.easy.Project method)
iter_steps() (railroadtracks.hortator.PersistentTaskGraph method)
iter_targetassets() (railroadtracks.easy.Project method)
M
model (railroadtracks.easy.Project attribute)
N
name (railroadtracks.easy.ActivityCount attribute)
new (railroadtracks.hortator.DbID attribute)
newproject (railroadtracks.easy.Project attribute)
P
persistent_graph (railroadtracks.easy.Project attribute)
PersistentTaskGraph (class in railroadtracks.hortator)
PersistentTaskGraph.StoredEntityNoLabel (class in railroadtracks.hortator)
Project (class in railroadtracks.easy)
provenancewalk_storedentity() (railroadtracks.hortator.StepGraph method)
R
railroadtracks.easy (module)
railroadtracks.hortator (module)
railroadtracks.rnaseq (module)
railroadtracks.unifex (module)
S
status (railroadtracks.easy.ActivityCount attribute)
statuslist (railroadtracks.hortator.PersistentTaskGraph attribute)
Step (class in railroadtracks.hortator)
step_concrete_state() (railroadtracks.hortator.PersistentTaskGraph method)
stepclasses (railroadtracks.easy.Environment attribute)
stepconcrete_dirname() (railroadtracks.hortator.StepGraph static method)
StepGraph (class in railroadtracks.hortator)
stepinstances (railroadtracks.easy.Environment attribute)
T
TaskStatusCount (in module railroadtracks.hortator)
U
unified_exec_run() (in module railroadtracks.unifex)
V
version (railroadtracks.hortator.PersistentTaskGraph attribute)
W
wd (railroadtracks.easy.Project attribute)